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- PDB-9k1u: crystal structure of Rtks and Ppka complex -

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Basic information

Entry
Database: PDB / ID: 9k1u
Titlecrystal structure of Rtks and Ppka complex
Components
  • Serine/threonine protein kinase
  • Type VI secretion system-associated protein
KeywordsSIGNALING PROTEIN / Rtks
Function / homology
Function and homology information


protein serine/threonine kinase activity / ATP binding / membrane
Similarity search - Function
Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / Serine/threonine protein kinase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.792 Å
AuthorsXu, M. / Ran, T. / Wang, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770074 China
CitationJournal: To Be Published
Title: crystal structure of Rtks and Ppka complex
Authors: Xu, M. / Ran, T. / Wang, W.
History
DepositionOct 16, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Type VI secretion system-associated protein
D: Serine/threonine protein kinase
A: Type VI secretion system-associated protein
B: Serine/threonine protein kinase


Theoretical massNumber of molelcules
Total (without water)68,7654
Polymers68,7654
Non-polymers00
Water2,468137
1
C: Type VI secretion system-associated protein
B: Serine/threonine protein kinase

D: Serine/threonine protein kinase

A: Type VI secretion system-associated protein


Theoretical massNumber of molelcules
Total (without water)68,7654
Polymers68,7654
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area7120 Å2
ΔGint-29 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.552, 107.459, 54.322
Angle α, β, γ (deg.)90.00, 107.91, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Type VI secretion system-associated protein


Mass: 24424.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: DMW43_01670, I8391_000023 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2V4GN18
#2: Protein Serine/threonine protein kinase


Mass: 9958.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: C3R40_03310 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAP8TYK6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.56 Å3/Da / Density % sol: 21 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.792→50 Å / Num. obs: 39167 / % possible obs: 99.4 % / Redundancy: 5.5 % / CC1/2: 0.996 / Rpim(I) all: 0.036 / Net I/σ(I): 34.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1941 / CC1/2: 0.514 / Rpim(I) all: 0.62 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9K0L

9k0l


Resolution: 1.792→37.25 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2428 3887 5.09 %
Rwork0.1985 --
obs0.2008 39128 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.792→37.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3974 0 0 137 4111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084076
X-RAY DIFFRACTIONf_angle_d1.1095550
X-RAY DIFFRACTIONf_dihedral_angle_d5.952557
X-RAY DIFFRACTIONf_chiral_restr0.067602
X-RAY DIFFRACTIONf_plane_restr0.01747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.792-1.810.39981180.35272286X-RAY DIFFRACTION84
1.81-1.840.38971380.3332453X-RAY DIFFRACTION93
1.84-1.860.33591360.3032516X-RAY DIFFRACTION97
1.86-1.890.32131300.28942593X-RAY DIFFRACTION98
1.89-1.910.28891500.28122610X-RAY DIFFRACTION99
1.91-1.940.30431430.25792640X-RAY DIFFRACTION98
1.94-1.970.2911300.25542543X-RAY DIFFRACTION99
1.97-20.32421520.24512658X-RAY DIFFRACTION99
2-2.040.34811250.24782607X-RAY DIFFRACTION99
2.04-2.080.2951520.22582605X-RAY DIFFRACTION99
2.08-2.120.22521510.22922568X-RAY DIFFRACTION99
2.12-2.160.26941340.21892677X-RAY DIFFRACTION99
2.16-2.210.26351430.22672540X-RAY DIFFRACTION99
2.21-2.260.30211280.22522655X-RAY DIFFRACTION99
2.26-2.310.2791490.21912580X-RAY DIFFRACTION99
2.31-2.380.27911230.22022619X-RAY DIFFRACTION99
2.38-2.450.26751420.23432643X-RAY DIFFRACTION99
2.45-2.530.29191320.22092616X-RAY DIFFRACTION99
2.53-2.620.28361620.22942582X-RAY DIFFRACTION99
2.62-2.720.22671340.21742674X-RAY DIFFRACTION99
2.72-2.840.36341280.21742582X-RAY DIFFRACTION99
2.84-2.990.23731390.21692633X-RAY DIFFRACTION99
2.99-3.180.26171540.20182610X-RAY DIFFRACTION99
3.18-3.430.29261300.18532598X-RAY DIFFRACTION99
3.43-3.770.20661470.17812625X-RAY DIFFRACTION99
3.77-4.320.17011350.16722614X-RAY DIFFRACTION98
4.32-5.430.19661480.15892575X-RAY DIFFRACTION98
5.44-37.250.23321340.18092563X-RAY DIFFRACTION97

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